Variant report

Variant	rs1539143
Chromosome Location	chr1:203372485-203372486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:203372032..203373841-chr1:203378581..203380625,2	MCF-7	breast:

Extended variants
information (count: 4 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10800929	0.84[EUR][1000 genomes]
rs1935171	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971219	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6428010	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1539143	KISS1	cis	parietal	SCAN
rs1539143	NEK7	cis	cerebellum	SCAN
rs1539143	SOX13	cis	parietal	SCAN
rs1539143	NAV1	cis	cerebellum	SCAN
rs1539143	UBE2T	cis	parietal	SCAN
rs1539143	PPP1R12B	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:203365400-203375000	Weak transcription	Right Atrium	heart
2	chr1:203369400-203373600	Enhancers	Fetal Lung	lung
3	chr1:203370200-203372800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:203370200-203372800	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr1:203370200-203373000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:203370200-203373000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:203370400-203372800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:203370400-203372800	Enhancers	Placenta	Placenta
9	chr1:203370400-203372800	Enhancers	Rectal Smooth Muscle	rectum
10	chr1:203370400-203373000	Enhancers	Colon Smooth Muscle	Colon
11	chr1:203370400-203374200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:203370600-203372600	Enhancers	Brain Hippocampus Middle	brain
13	chr1:203370600-203372600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr1:203370600-203372800	Enhancers	Brain Cingulate Gyrus	brain
15	chr1:203370600-203372800	Enhancers	NHDF-Ad	bronchial
16	chr1:203370600-203373000	Enhancers	Ovary	ovary
17	chr1:203370600-203373400	Enhancers	Fetal Stomach	stomach
18	chr1:203370600-203373600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:203370800-203372600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr1:203370800-203373000	Enhancers	Adipose Nuclei	Adipose
21	chr1:203370800-203373200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:203370800-203375000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:203371000-203372800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:203371000-203373000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:203371000-203375200	Weak transcription	Lung	lung
26	chr1:203371200-203372600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:203371200-203372600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:203371200-203372600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:203371200-203372600	Enhancers	Brain Substantia Nigra	brain
30	chr1:203371200-203372800	Enhancers	Brain Angular Gyrus	brain
31	chr1:203371200-203373000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:203371400-203372800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:203371400-203373000	Enhancers	Small Intestine	intestine
34	chr1:203371400-203374800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:203371400-203375000	Weak transcription	Fetal Intestine Large	intestine
36	chr1:203371400-203377600	Weak transcription	Left Ventricle	heart
37	chr1:203371600-203372600	Enhancers	Fetal Kidney	kidney
38	chr1:203371600-203372800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:203371600-203373000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr1:203371600-203374800	Weak transcription	Fetal Intestine Small	intestine
41	chr1:203371600-203375000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:203372000-203372800	Active TSS	Fetal Brain Male	brain
43	chr1:203372000-203374200	Weak transcription	Stomach Mucosa	stomach
44	chr1:203372200-203372800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:203372200-203373000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:203372200-203373000	Enhancers	Spleen	Spleen
47	chr1:203372200-203373000	Flanking Active TSS	NHLF	lung
48	chr1:203372200-203377400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:203372200-203377600	Weak transcription	HMEC	breast
50	chr1:203372400-203372600	Enhancers	Brain Anterior Caudate	brain

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